Merge pull request #6 from pd321/develop

Fixes #4 and #5

src/align.smk

@@ -6,17 +6,19 @@ rule trimgalore_se:
 	params:
 		quality = config['trimgalore']['quality'],
 		stringency = config['trimgalore']['stringency'],
-		e = config['trimgalore']['e']
-	# trimgalore does not recommend using more than 4 threads
-	threads: threads_mid if threads_mid < 4 else 4
+		e = config['trimgalore']['e'],
+		#trimgalore does not recommend using more than 4 threads
+		threads_actual = threads_mid if threads_mid < 4 else 4
+	# setting it to mid ensures not no many trimgalore jobs launched
+	threads: threads_mid
 	shell:
 		'trim_galore '
 		'--quality {params.quality} '
 		'--stringency {params.stringency} '
 		'-e {params.e} '
 		'--gzip '
 		'--output_dir results/bam/ '
-		'--cores {threads} '
+		'--cores {params.threads_actual} '
 		'--basename {wildcards.sample} '
 		'--no_report_file '
 		'{input} 2>&1 | tee {log}'
@@ -34,16 +36,19 @@ rule trimgalore_pe:
 	params:
 		quality = config['trimgalore']['quality'],
 		stringency = config['trimgalore']['stringency'],
-		e = config['trimgalore']['e']
-	threads: threads_mid if threads_mid < 4 else 4
+		e = config['trimgalore']['e'],
+		#trimgalore does not recommend using more than 4 threads
+		threads_actual = threads_mid if threads_mid < 4 else 4
+	# setting it to mid ensures not no many trimgalore jobs launched
+	threads: threads_mid
 	shell:
 		'trim_galore '
 		'--quality {params.quality} '
 		'--stringency {params.stringency} '
 		'-e {params.e} '
 		'--gzip '
 		'--output_dir results/bam/ '
-		'--cores 4 '
+		'--cores {params.threads_actual} '
 		'--basename {wildcards.sample} '
 		'--paired --no_report_file '
 		'{input[0]} {input[1]} 2>&1 | tee {log}'

src/se.smk

@@ -5,7 +5,7 @@ rule rose_main:
 		peaks = rules.blklist_filt.output
 	output:
 		enhancers_table = "results/se/{chip_sample}/{chip_sample}_peaks_AllEnhancers.table.txt",
-		enhancers_plot = "results/se/{chip_sample}/{chip_sample}_Plot_points.png"
+		enhancers_plot = "results/se/{chip_sample}/{chip_sample}_peaks_Plot_points.png"
 	threads: threads_mid
 	log: "logs/se/{chip_sample}_rose_main.log"
 	params: